The Battle That Broke The Rayquaza's Back
by finalfantasyt
Summary: Rayquaza continues on it's rampage with the destruction of Celadon. Brendan and May decide to travel to Ever Grande City, and meet some mysterious strangers.
1. Chapter 1

**Disclaimer: I do not own Pokemon**

It was a bright morning as Rayquaza flew through the skies of Hoenn.

_I hope no humans show up today,_ it thought. _Their countless losses to me are annoying._ The huge snake-like pokemon coiled atop the sky pillar, its favorite hangout and settled in for a nap.

_2 days later......_

"What is that?!" exclaimed a boy, upon seeing Rayquaza.

_Another human?_ Thought Rayquaza, opening one eye.

The boy threw a pokeball and a winged dragon came out. "Go! Salamence!"yelled the boy.

_Enough with this! I am tired of humans barging into my territory and attacking me! They think they own the world! Well, I've got something to say about that! _Rayquaza screamed in its mind. It uesd Outrage and blindly attacked Salamence. Salamence instantly collapsed.

"Ah! Uh...go! Blaziken!" The fire pokemon came out and assumed a fighting pose.

_Die!_ Was Rayquaza's mental response, crushing Blaziken. Again, and again, Rayquaza beat the living daylights out of the boy's pokemon, until at last, he ran out.

"Oh no! I have to run!" gasped the boy.

_You won't escape!_ Thought Rayquaza, still fired up. Before the boy could move, he was hit by Hyper Beam, and was blasted off the tower. His lifeless body fell into the ocean, forever.

_Pacifidlog Town_, _1 week later..._

"Nurse Joy! Nurse Joy! Come quickly!" called a man, while running from the beach.

"What is it?" she asked walking to the window of the pokemon center. "Oh my!" she exclaimed. The man was holding the body of a boy. The body was bleeding in too many places to count, and he was missing an arm. His clothes had been reduced to rags.

"I found him washed up on the beach" explained the man.

"How could this happen?" said Nurse Joy. She helped the man bring the body to the hospital. "All of his bones seem to be broken. His lungs have been crushed and he seems to have suffocated to death. But how could he have been attacked? The only thing capable of doing this is a pokemon" summarized Joy, with a nervous look on her face.

"Apparently, this pokemon does attack humans. And it attacks to kill" stated the man.

"If that's true....than all humans are in danger" whispered Nurse Joy. She sighed, and looked out the window, worried.

_Somewhere over Johto..._

_Humans have ruled us for too long! _raged Rayquaza as it sped past Cianwood town. _I will search all over for others like me. Then, the humans will be doomed!_ It spotted a group of islands. _I will begin there_, it thought, and flew down to the island caves.

_Route 121, 9 hours later..._

May was walking through a forest, near Lilycove city. _I need to find some new pokemon before challenging the Sootopolis gym, _she thought. As she was walking, she noticed a large sign.

"Safari Zone: Enjoy lots of rare pokemon for our low prices!" was written on the sign.

"I'll try in there," she said quietly. She walked past the friendly guard and paid. He gave her 30 Safari Balls and a friendly wave. She walked into the Safari Zone and started looking for pokemon.

_Mt. Silver_

Rayquaza was flying past Mt. Silver. A crazy grin inhabited his face. It had persuaded Ho-oh, Entei and Raikou. The four of them were going to Kanto. After getting a few more allies, they would attack.

_This is it! We will finally crush all humans! _Thought Rayquaza. _They will be powerless against our combined might! Already, I have recruited 3 other titans. Two or three more and we will be unstoppable! _The pokemon moved off into the Kanto region.

_Mossdeep City, 1 day later..._

Brendan was finishing his meal. He had decided to eat while waiting for the ship to Sootopolis. The sun was setting in the distance. He cleaned up and threw away his garbage. As he was walking through town, he heard some people talking.

"Yes, my pokemon seem to be scared too," said a woman. "But why?"

"Well, maybe they are sensing some kind of danger," said a man.

_Danger?_ Thought Brendan. _It has always been peaceful in Hoenn_, he reasoned. His thoughts were interrupted by a ship's horn. "Ah, my ship is here," said Brendan. He boarded and walked onto the deck. _1 more badge..._ he thought.

_Unknow_n _Dungeon, outskirts of Cerulean City..._

Rayquaza's group was heading through the Unknown Dungeon. Articuno was now with them, and they hoped to find an ally in this dark place. At last, they found a large platform. In the center was a somewhat humanoid creature. It had a large purple tail, short white fur and dark eyes.

"Why have you come here?" asked the creature. It spoke in their minds instead of aloud.

After they explained, the creature nodded. "I am called Mewtwo, and I will give you assistance," it replied.

_We have enough! _thought Rayquaza. "We attack tomorrow. Our first target: Saffron City," it announced. _Our time has come! _Thought Rayquaza. _The reign of pokemon begins!_ It went to sleep thinking deathly thoughts.

_Lilycove Harbor, 9:00 P.M._

May stepped onto the ship. She was taking the late ship to Sootopolis. She had been successful in capturing several bug and grass pokemon and Pikachu. She was hoping to use the Pikachu in her battle against Wallace because she had heard that he used water pokemon. She walked through the ship and admired the fancy wallpaper. She found her room and laid down for a nap.

_Sootopolis City, the next morning..._

Brendan was walking to the Sootopolis Gym. His ship had just arrived. He had stopped at the pokemon center to heal his pokemon, and to stock up on supplies. He walked past the beautiful lake and into the gym. "Wallace! I challenge you!" he called.

"Fine. We will each use five pokemon. Agreed?"

"Agreed," replied Brendan. He threw a great ball. A Manectric popped out and crouched, ready for battle. Wallace had chosen Seadra.

"An electric pokemon. Good choice! However, I won't go down easily!" said Wallace.

_A small platform in the depths of Unknown Dungeon..._

Rayquaza opened one eye. Then the other. The other titans seemed to be awake already. Rayquaza thought for a moment, then said "If any of us are caught, the rest of us must free that one. Agreed?" The rest of them muttered their agreement. "Then we go! To Saffron City!" shouted Rayquaza. The pokemon traveled through the cave to the beginning, where they met two shadowy figures.

The big red one had long claws, and spikes on its neck. It also seemed to have spikes on its tail. "I am called Groudon. I have heard of what you are doing and wish to help," proclaimed Groudon.

The blue one was in the water. It had huge fins, and a small mouth full of razor-sharp teeth. "I am Kyogre, and I, too, wish to join you," said Kyogre. Now with two more members, the group passed Cerulean City and closed in on Saffron.

_Sootopolis City, the Pokemon Gym_

Brendan was down to Swampert and Wallace had only Milotic. Seaking had defeated Manectric with Horn Drill, and Brendan's other pokemon weren't as strong. Swampert had defeated Seaking, so it was one-on-one. "Milotic, Ice Beam!" called Wallace.

"Swampert, Earthquake!" ordered Brendan. Both Milotic and Swampert were badly injured after that round of attacks, so Brendan yelled "Finish this, Swampert! Mud Shot!" Swampert fired a stream of mud, and Milotic collapsed.

"You defeated me...fine. Take this badge. You've earned it," said Wallace.

"Thank you," replied Brendan, taking the badge. "Swampert, return!" he said. Swampert came back to it's pokeball in a stream of red light. Brendan triumphantly walked out of the gym.

Back in the pokemon center, Brendan spied a pile of newspapers. He picked one up and read the headline, "Mysterious Pokemon travel through Johto." The article claimed that a group of mysterious and rare pokemon had crossed through the area, but had avoided all signs of civilization.

""Interesting..."he muttered. "Nurse Joy," he called. "How can I get into Johto?"

"Well..." she replied, "I think you can hike through the mountains near Ever Grande City."

"Is there any other way?" questioned Brendan.

"You could get back to Slateport, and get a ship from there, but that would probably take longer." she replied.

"Yeah," muttered Brendan. "Well, thanks," he called, as he walked out of the Pokemon Center.

"No problem," called back Nurse Joy.

Brendan glanced down at the paper again. Another headline, below the first one, caught his eye. "Boy Mortally Injured From Another Cause," read the headline. "Weird," said Brendan. He read on to find out that only a pokemon could have hurt the boy. "But ... pokemon don't kill people," said Brendan. "I mean, they may get mad and rough up a human a bit, but a pokemon that kills people?" He shook his head. "Maybe Johto has answers."

He arrived at the harbor and started looking for a ship to Ever Grande City.

_Saffron City, Train Station_

A man walked up to the train guard. "Here's my rail pass," he said, bringing out a card.

"Yes sir," replied the guard. "The magnet train – ." He was cut off by Rayquaza's Hyper Beam destroying the train. "- is currently experiencing some technical difficulties. Please come back," said the guard as he eyed the remains of the train.

The man and the guard ran outside to find the city under attack. The people of Saffron City tried to use their pokemon, but it was useless. The legends crushed any and all opposition.

Within an hour, the city was destroyed. All of it's inhabitants had either fled, or were lying dead in the streets. There were no survivors.

"Perfect," snickered Rayquaza, coiling around the Silph Company building. It eyed the destruction around it with a sick grin.

"Allow me to choose our next target," said Mewtwo, floating up to rest beside Rayquaza.

"Sure," replied Rayquaza. "What do you have in mind?"

"Celadon City. There is a man there named Giovanni. He tried to control me, and I want revenge!" came Mewtwo's forceful reply.

"Revenge...a worthy cause," decided Rayquaza. "Let's find the others, so that we can get to the next stop on our killing spree." With that delightful statement, the two parted and went to find the others.

_A ship, in Sootopolis Harbor_

May was awakened by the announcement "We have now arrived in Sootopolis City." She yawned, and sat up. It was around 3:00 P.M., judging from the sun's position. She collected her belongings, and exited the ship. She made sure that her pokemon were ready and entered the Sootopolis gym.

"I expect you want a battle," greeted Wallace. "So, let's begin!" He brought out his Seadra, and May chose Pikachu. However, Seadra used Twister, which trapped Pikachu inside.

"Pikachu, use your Quick Attack to escape!" suggested May. The small electric mouse responded and broke through. "Now, Thunderbolt!" called May. Pikachu glowed with energy and released a powerful bolt. Seadra was fried, and it collapsed.

After calling back Seadra, Wallace released Sealeo from it's pokeball. "Sealeo, Body Slam!" yelled Wallace. The fat seal pokemon reared up and crushed Pikachu. It seemed like Pikachu was down, but suddenly, Sealeo was encased in an electric field. Sealeo fell over, defeated. "Interesting...that is one determined Pikachu!" exclaimed Wallace. "Go, Gyrados!" he said, tossing another pokeball. A huge sea serpent came out and reared over Pikachu. "Hydro Pump!" said Wallace, with finality in his voice. Huge streams of water blasted through the air and hit Pikachu. Pikachu was thrown against the wall, where it lay, unmoving.

"Pikachu, return!" called May. After thinking for a moment, she said "Go, Nosepass!" The strange rock pokemon emerged and faced Gyrados. "Nosepass," she yelled, "Rock Tomb!" Rocks exploded from all around Gyrados and trapped it. Gyrados seemed to be trapped, but after a moment or two, it broke free of the rocks and glared at Nosepass.

"Gyrados, Hyper Beam!" commanded Wallace. A huge beam of pure energy shot from Gyrados' mouth and smashed into Nosepass. Nosepass fell, but shakily got to its feet.

"Nosepass, hit it with Rock Throw and Rock Tomb at the same time!" cried May. Large rock pillars erupted from around Gyrados, and rocks fell from the ceiling, crushing it. May waited with baited breath as the rocks trembled with Gyrados' rage, but at last the trembling ceased.

"Gyrados, return!" called Wallace, looking worried. "Go, Seaking!" The large fish pokemon landed gracefully in the water and began swimming around Nosepass.

"Nosepass, use Rock Throw!" said May quickly.

"Seaking, go under water!" said Wallace, equally quick. Seaking did not emerge from the water, but Wallace seemed confident. "Now Seaking, come up!" said Wallace abruptly. Seaking came up and blasted Nosepass with water. Without stopping, she also hit Nosepass with her horn. This combo was too much for the weakened Nosepass, which instantly fainted.

"Oh no..." mumbled May. After recalling Nosepass, she chose Bellossom. The flower pokemon immediately started dancing. "Bellossom, charge up for a Solar Beam!" ordered May.

Wallace frowned, then said "Seaking, use Horn Drill!" Seaking tried to ram Bellossom, but Bellossom evaded her. "Seaking, try one more time!" yelled Wallace.

At the same time, May called "Bellossom, go!" As Seaking crashed into Bellossom, Bellossom used Solar Beam for a small explosion. When the dust cleared, both pokemon were lying there defeated. May recalled Bellossom as Wallace recalled Seaking. Wallace released his final pokemon, Milotic, as May released Xatu.

"Milotic, Ice Beam!" yelled Wallace. Xatu tried to dodge, but it was too late. Xatu was frozen solid.

"Only one left..." mumbled May unhappily. "Go, Blaziken!" Blaziken came out and stared grimly at Milotic.

"A fire pokemon?" exclaimed Wallace, surprised. "Milotic, Water Gun!" A spurt of water came from Milotic's mouth and almost defeated Blaziken. Suddenly, May remembered something she had read. There were supposed to be three legendary attacks, one for fire, one for grass, and one for water. Her only chance...

_Well, _she thought, _here goes._ "Blaziken, Blast Burn!" she yelled.

"What?!" exclaimed Wallace. Fire radiated from Blaziken and the room was consumed in fire. When the fire was gone, Milotic crashed to the ground at his feet. "Amazing...well, here's your badge," he said to May. She took the badge, and wandered out into the city, amazed.

_Well, I better get going. _She wandered onto the dock, happy to be alive.


	2. Chapter 2

Sorry for the bad ending; I was a bit rushed. Thanks to everyone who reviewed. Also, I'm really sorry for not posting for so long.

Ice-Phoenix-chan: Thanks for the suggestions and the compliments. I will try to add more details.

surfingpikachu05: Thanks.

Facia: Thanks for the advice. I was a bit rushed. I will try to reveal the pokemon's motives in this chapter.

Story Weaver1: Thanks. Also, Wallace is the eighth gym leader. Did you confuse him with Wally?

Wandering Gamer: Thank you. A few legendaries _might_ join the humans. I haven't decided.

**Disclaimer: I don't own Pokemon. I do own any original characters and the plot.**

_The remains of Saffron City_

Sabrina was coming home after a week's vacation. She had left the gym for a bit of fresh air, but she was ready to resume being the leader. _There it is,_ she thought, brushing her long black hair out of her face. _Saffron City is just over that hill._ She got to the top of the hill and almost fainted. Saffron City was gone. Most of the buildings had been destroyed. The only one left was the Silph Company building. Sabrina fell to her knees. _This is impossible..._ she thought. _I knew many of the people here...they were very good trainers. How could the whole city be destroyed? _She got to her feet. _I will not let this go unnoticed!_ She turned around, and began the walk to Lavender Town.

_Route 7_

"Let's destroy the department store first!" snickered Groudon.

"Sure. Then let's get the mansion!" replied Entei. Groudon had helped Entei defeat a tough Poliwrath in Saffron, and the two became "war buddies" after that.

"Whatever," said Mewtwo, floating beside them. "Just leave the Game Corner to me." It floated off toward the front of the group.

Entei and Groudon shrugged and continued on their way. "So, why did you join?" asked Groudon.

"I joined because of Rayquaza's reasoning," explained Entei. "I am tired of humans thinking that they own pokemon. Also, I want to be able to roam freely, without the threat of humans."

"I joined because of...them," stated Groudon, mysteriously.

"Who?" asked Entei, curious.

Groudon shook it's head. "It doesn't matter," it said. "I will get revenge when we reach Hoenn."

At that precise moment, the group saw Celadon City. The tall buildings loomed out of the wilderness. "What's our strategy?" asked Raikou.

Rayquaza opened its mouth, but Mewtwo answered quicker; "We surround the city and attack from all directions." The group fanned out around the city and took their positions."Go," said Mewtwo, telepathically.

Kyogre was poised behind the gym. While it could live without water, it didn't like being dry. When Mewtwo gave the signal, it burst out and started attacking._ Is it really necessary to take innocent lives?_ It asked itself. _I guess...humans need to be taken care of and I see no alternative._

Erika rushed out of the gym. "What's going on?!" she cried.

"Erika!" called one of her assistants. "We're under attack!" At that very moment, a stream of fire went through the roof on the gym. Erika looked back, horrified. The gym caught fire, as people rushed into the streets. Erika looked to the edge of town, but a ray of pure ice was sealing off the exits. _Well, _she thought, _I guess I must fight._

"Go, Tangela!" she called, releasing a mess of green vines. No sooner had Tangela appeared then Articuno swept out of the sky and froze it.

Erika winced. "Go Gloom!" she yelled. The flower pokemon came out and looked around. "Gloom, Stun Spore on that red, spiky one!" she added. The red spiky one (Groudon) was just about to torch the mansion, when it was locked in place.

_What?_ it thought. _I can't move!_ It struggled, but to no help.

"Now, Razor Leaf!" The sharp leaves came from all around and cut Groudon. Suddenly, a burst of flames came from the right. Entei ran up to Gloom and fried it.

"Now we're even," it said to Groudon. Groudon nodded.

"Go–" but Erika never got to choose another pokemon. Groudon had regained its movement, and she was consumed by its flames of anger.

_Sootopolis Harbor_

May walked along, still amazed at her good fortune. _Blast Burn exists?_ she thought. _I thought it was a myth...and furthermore, how can I use it?_ Just then, she heard a familiar voice.

"May!" She looked around and spotted her childhood friend.

"Brendan! It's been a while," replied May. "I just defeated Wallace, and got the eighth badge!"

"Me too!" exclaimed Brendan. "By the way, where are you headed next?"

"I don't know," she replied.

"I'm going to Ever Grande City. Then I'm going to hike to Johto. Do you want to come?" he asked hopefully.

"Umm...sure," she replied. "I haven't got anywhere else to go," she stated.

"Great! The ferry gets here in about an hour. Let's go get some tickets," said Brendan, grinning.

The two trainers walked off to the ticket booth, thinking about the journey ahead. _56 minutes later..._

"Look! There's the ferry!" pointed May. Brendan looked up. Sure enough, the big white ship was sailing into port. "C'mon, let's go!" she said, jumping up. May and Brendan walked up to the ship, as the boarding stairs were lowered. They headed up the steps and onto the ship.

"Let's see..." said Brendan. "My room number is 121..."

"Mine is 126," said May. "So, I guess we're in the same hall."

"Well, I'm tired," yawned Brendan. "I need to go to sleep."

"Okay, see ya!" replied May, and the two walked into their respective rooms.

Brendan observed his room. It seemed to be a typical room; it had a bed, a chair, a clock and a window. He put his bag on the chair, stretched out on the bed, and went to sleep.

May didn't feel like sleeping. She put her pack on the bed, and walked off to explore the ship. As she was walking past various cabins, she noticed some stairs. She climbed them, and ended up on the top deck. The powerful wind almost caused her to lose her balance, but she gripped the railing. The ship was moving at an incredible pace; the waves went by constantly. A sailor walked up behind her, and saw the pokeballs on her belt.

"Ah, a trainer, are you?" asked the sailor. "Care to battle, lass?"

May turned around. "Sure!" she replied. "1-on-1?" she asked.

"Fine with me," said the sailor. "Go, Poliwhirl!"

"Bellossom, your turn!" called May, tossing a pokeball. _That's odd...I've never seen that pokemon before..._she thought, looking at the poliwhirl (A/N: Remember, May has never left Hoenn, so she hasn't seen all the pokemon).

Noticing May's puzzled look, the sailor laughed. "I got him in a trip to Kanto," he explained.

"Oh...well, I'll hit him so hard, he'll be knocked back to Kanto! Bellossom, Razor Leaf!" she replied. Bellossom began to dance, and leaves shot toward Poliwhirl. However, before the leaves hit, a strong wind blew them away. "What?!" cried May.

"If you're going to battle on a ship, you should consider the weather," the sailor explained. "Around here, we get lots of wind, so projectile attacks are not very effective," he said. "Poliwhirl, Dynamic Punch!" he finished. Poliwhirl leapt into the air and used it's feet to push off the mast. It dove down and delivered a crushing blow right to the face.

"Bell..oss..om," cried the pokemon, as it was smashed into the wall.

"No..." said May. Bellossom struggled to stand.

"It's still conscious?" said the surprised sailor. "Any normal pokemon would be out for good after a blow like that..."

"Bellossom, try a Hyper Beam!"

"Hyper Beam?! Darn it..." said the sailor."Poliwhirl, counter with your Surf!" he called. A wave of water crashed into the pillar of energy, and a flash of light temporary blinded the two pokemon. The trainers watched with baited breath as the flash took place. _Come on Bellossom..._thought May. When the light faded away, the trainers rushed to examine their pokemon.

"Oh no....Bellossom fainted...." mumbled May.

"Interesting....very interesting....." said the sailor, examining Poliwhirl. "It seems we have a draw..." he continued.

"Really? May, have you gone soft?" Brendan walked up, shaking his head.

"Hey, this guy's pretty good," said May defensively. "You battle him," she challenged.

"Alright," said Brendan. "Okay with you?" he asked the sailor.

"Yeah, fine," he replied, and used a Revive on Poliwhirl. "One-on-one okay with you?" he asked Brendan.

"That's fine," confirmed Brendan. "I think I'll use Swellow." He released the bird pokemon. It flew up and circled his head, before landing on a rail.

"Poliwhirl, use your Hypnosis!" called the sailor. Poliwhirl tried to lock eyes with Swellow, but it was too fast.

"Now, Swellow, Aerial Ace!" said Brendan. Swellow swooped up and shot down. It passed Poliwhirl in an instant, and it's speed cut Poliwhirl's arm and stomach.

"Don't let it faze you! Use Strength!" countered the sailor. Poliwhirl jumped after the bird and gave it a powerful punch to the back. Swellow lost control and careened toward the wall.

"Swellow, don't lose focus!" called Brendan. Swellow skimmed the wall and shot back toward Poliwhirl. Poliwhirl tried to punch it again, but Aerial Ace was too quick. Some more blood spurted out of Poliwhirl's arm and it stumbled back.

"Hmm..." muttered the sailor, thinking. "Poliwhirl, Surf!" The pokemon shot a jet of water at Swellow. The bird took it full force, and struggled to stay in the air. It was clear to Brendan that he if the battle didn't end now, Swellow would lose.

"Swellow, finish this! Fly!" said Brendan.

"Strength, quickly!" yelled the sailor, but it was too late. Swellow had turned and flew up as high as it could go. Then, it turned and dived down, smashing into Poliwhirl's head and knocking it out.

"Hah! I win!" Brendan grinned.

"Well, that was a good match. I'd like to battle trainers like you two more often," said the surprised sailor. "I'm Doregard (A/N: My friend made this name and he wanted me to use it. It's kinda weird, but kinda funny too). Who are you?"

"I'm May," said May.

"And I'm Brendan," said Brendan.

"I better get back to work, but it was nice meeting you two. Maybe we'll see each other again." With that, Doregard waved and walked off.

"So, how've you been?" asked Brendan.

"Okay, and you?" replied May.

"I'm good. By the way, did you read about that killer pokemon?" asked Brendan.

"A killer pokemon?! I've never heard of it. What happened?" asked May.

"Well, I read in _The Sootopolis Times_ that a boy was discovered dead, and they suspect a pokemon did it," replied Brendan.

"Huh, weird," said May. The two trainers continued to chat throughout the trip.

_Ever Grande City Harbor_

May and Brendan walked off the ship. After buying supplies at the nearby pokemart, they set off on a trail through the mountains. "So, how long are we gonna be hiking?" asked May.

"Well, according to this guidebook, it should take a week or two," replied Brendan.

After they had been hiking for a little while, they heard a voice.

"Stop. These are our mountains." The voice belonged to a boy who looked to be about 15.

"If you want to get through, you must beat us." A man was standing next to the boy (A/N: These guys are both OCs).

"And if you lose...you die..."

_To be continued..._


End file.
